Use this tool to extract metadata from microscopy formats supported by Bioformats and convert to OME-XML.
Because CZI format stores multiple resolutions as different Image tags, by default the ouput will be only first Image tag in the metadata.
Examples:
XML output:
java -jar extract_meta.jar raw_microscopy.czi output.xml
Will dump OME-XML metadata from CZI image to XML file
XML output with remapping:
java -jar extract_meta.jar raw_microscopy.czi output.xml mapping.yaml
Will replace Channel attributes Fluor, Name, SizeX, SizeY and dump OME-XML metadata from CZI image to XML file
Replace OME metadata in OME-TIFF
java -jar extract_meta.jar raw_microscopy.czi output.ome.tiff
Will replace metadata in the existing OME-TIFF file with metadata from raw file converted to OME-XML, or if output.ome.tiff does not exist will convert raw file to OME-TIFF.
Replace OME metadata in OME-TIFF with remapping
java -jar extract_meta.jar raw_microscopy.czi output.ome.tiff mapping.yaml
Will replace Channel attributes Fluor, Name, SizeX, SizeY of metadata from raw file and put this new metadata in the existing OME-TIFF file, or if output.ome.tiff does not exist will convert raw file to OME-TIFF.
Dump all metadata from CZI to OME-XML
java -jar extract_meta.jar raw_microscopy.czi output.xml --nochanges
Will dump metada without modifying it.